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Finding relations between genes and diseases is essential in developing a clinical diagnosis, treatment, and drug design for diseases. One successful approach for mining the literature is the document-based relation extraction method. Despite recent advances in document-level extraction of entity-entity, there remains a difficulty in understanding the relations between distant words in a document. To overcome the above limitations, we propose an AI-based text-mining model that learns the document-level relations between genes and diseases using an attention mechanism. Furthermore, we show that including a direct edge (DE) and indirect edges between genetic targets and diseases when training improves the model's performance. Such relation edges can be visualized as graphs, enhancing the interpretability of the model. For the performance, we achieved an F1-score of 0.875, outperforming state-of-the-art document-level extraction models. In summary, the SCREENER identifies biological connections between target genes and diseases with superior performance by leveraging direct and indirect target-disease relations. Furthermore, we developed a web service platform named SCREENER (Streamlined CollaboRativE lEarning of NEr and Re), which extracts the gene-disease relations from the biomedical literature in real-time. We believe this interactive platform will be useful for users to uncover unknown gene-disease relations in the world of fast-paced literature publications, with sufficient interpretation supported by graph visualizations. The interactive website is available at: https://ican.standigm.com. [ABSTRACT FROM AUTHOR]

Background: The coexistence of Graves' disease with thyroid cancer is well-known and total thyroidectomy is recommended in such cases. However, Graves' disease might be dormant at the time of surgery and diagnosed after lobectomy for thyroid cancer. Methods: We assessed the incidence and clinicopathological characteristic of newly developed Graves' disease after lobectomy for thyroid cancer between 2010 and 2019. Results: In all, 11043 patients underwent lobectomy for thyroid cancer during the study period, and 26 (0.2%) were diagnosed with Graves' disease during follow-up. The median age was 43.8 years, 88.5% were female, and all were euthyroid before surgery. The median time from lobectomy to the diagnosis of Graves' disease was 3.3 years. Half of the patients were diagnosed based on thyroid function tests during routine follow-up, and others were diagnosed due to symptoms of thyrotoxicosis. Among patients who had checked preoperative thyroid autoantibodies, 61.1% showed positivity. Twenty-one (80.8%), and 2 (7.7%) patients received antithyroid drugs and radioactive iodine therapy, respectively, and 3 (11.5%) underwent completion thyroidectomy. Conclusion: Although rare, Graves' disease can occur in the remnant thyroid after lobectomy. Such patients are more likely to have autoantibodies. An appropriate workup is required when hyperthyroidism is found during the follow-up of patients after lobectomy. [ABSTRACT FROM AUTHOR]

Background: The follicular variant of papillary thyroid cancer (FVPTC), especially the encapsulated non-invasive subtype, is a controversial entity. Recent study suggested using ‘non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)’ for these indolent carcinomas. We evaluated the impact of reclassification from non-invasive encapsulated FVPTCs (EFVPTCs) to NIFTPs in the diagnosis of thyroid nodules with architectural atypia. Methods: We reviewed 1301 thyroid nodules with architectural atypia in core needle biopsy (CNB) specimens obtained from March 2012 to February 2013. Nodules were classified into atypia of undetermined significance with architectural atypia (AUS-A, 984, 76%) or follicular neoplasm/suspicious for a follicular neoplasm (FN/SFN, 317, 24%). Among them, diagnostic surgery was performed in 384 nodules (30%). Results: In total, 160 nodules (42%) presented final malignant diagnoses including 39 non-invasive encapsulated FVPTCs (10%). The malignancy rate was estimated to be 7–35% in AUS-A nodules and 28–49% in FN/SFN nodules. After reclassification, the malignancy rate was much decreased and estimated to be 5–24% in AUS-A nodules, and 23–39% in FN/SFN nodules. Thyroid nodules with final malignant diagnoses were significantly more likely to have a FN/SFN CNB diagnosis, malignant US features and concomitant nuclear atypia in CNB specimens. However, these factors could not differentiate NIFTPs from other malignancies. Conclusions: After reclassification of non-invasive EFVPTCs to NIFTPs, the malignancy rate of thyroid nodules with architectural atypia in CNB specimens was decreased. However, there were no preoperative factors differentiating other malignancies from NIFTPs. The presence of malignant US features or concomitant nuclear atypia might help clinicians deciding diagnostic surgery but, these features also might indicate NIFTPs. [ABSTRACT FROM AUTHOR]

Background: Although patients with minimally invasive follicular thyroid carcinoma (MIFTC) generally have an excellent prognosis, distant metastasis occurs in some patients. Risk factors for distant metastasis have been reported, none has been found to be conclusive. This study evaluated risk factors for distant metastasis, including protein markers, in patients with MIFTC. Methods: A review of patient records identified 259 patients who underwent surgery at Asan Medical Center from 1996 to 2010 and were subsequently diagnosed with MIFTC. After review of pathological slides, 120 patients with paraffin blocks suited for tissue microarrays (TMA) were included in this study. Immunohistochemical stain of TMA slides was performed by protein markers; β-catenin, C-MET, CK19, estrogen receptor (ER) α, ER β, HBME-1, MMP2, PPAR γ and progesterone receptor. Results: 120 patients included 28 males (23.3%) and 92 females (76.7%), of mean age 41.5±10.8 years (range, 13–74 years). Eight patients (6.7%) had distant metastases during follow-up. Univariate analysis showed that age (≥45 years), male sex, and extensive vascular invasion (≥4 foci) were associated with distant metastasis. Multivariate regression analysis showed that extensive vascular invasion was the only independent risk factor for distant metastasis (p = 0.012). Although no protein markers on TMA analysis were directly related to distant metastasis of MIFTC, CK19 expression was more frequent in patients with than without extensive vascular invasion (p = 0.036). Conclusion: Extensive vascular invasion was the only independent risk factor for distant metastasis of MIFTC. No proteins markers were directly related to distant metastasis, but CK19 was associated with extensive vascular invasion. [ABSTRACT FROM AUTHOR]

Background: Ampulla of Vater cancer (AoV Ca) is a rare tumor, and its adjuvant treatment has not been established. The purpose of this study was to find out prognostic factors including host immunity and role of adjuvant treatment in AoV Ca. Methods and Findings: We reviewed 227 AoV Ca patients with curative resection. Clinical characteristics, adjuvant treatment, disease-free survival (DFS) and overall survival (OS) were analyzed. Among all patients, 63.9, 36.1 and 33.9% had T1/T2, T3/T4 stage and lymph node-positive disease (LN+), respectively. OS of all patients was 90.9 months (95% CI: 52.9–129.0). OS was different according to neutrophil-to-lymphocyte ratio (HR 1.651, 95% CI: 1.11–2.47), platelet-to-lymphocyte ratio (HR 1.488, 95% CI: 1.00–2.21) and systemic inflammatory index (HR 1.669, 95% CI: 1.13–2.47). In multivariate analysis, adverse prognostic factors for OS included vascular invasion (HR 2.571, 95% CI: 1.20–5.53) and elevated CA 19–9 (HR 1.794, 95% CI: 1.07–3.05). A total of 104 patients (46.3%) received adjuvant treatment (25 out of 111of T1/T2 & LN (-), 79 out of 116 of T3/T4 or LN (+)). In T3/T4 or LN (+) stage, adjuvant CCRT with maintenance chemotherapy provided the longest OS (5-year OS rate: 47.0 vs. 41.4%). Conclusions: Vascular invasion and elevated CA 19–9 were adverse prognostic factors in resected AoV Ca. In T3/T4 or LN (+) stage, adjuvant CCRT with maintenance chemotherapy provided the best survival outcome. Adjuvant treatment should be further defined in AoV Ca, especially with poor prognostic factors. [ABSTRACT FROM AUTHOR]

Introduction: Neutrophil to lymphocyte ratio (NLR) and standard uptake value (SUV) by 18F-FDG PET represent host immunity and tumor metabolic activity, respectively. We investigated NLR and maximum SUV (SUVmax) as prognostic markers in metastatic pancreatic cancer (MPC) patients who receive palliative chemotherapy. Methods: We reviewed 396 MPC patients receiving palliative chemotherapy. NLR was obtained before and after the first cycle of chemotherapy. In 118 patients with PET prior to chemotherapy, SUVmax was collected. Cut-off values were determined by ROC curve. Results: In multivariate analysis of all patients, NLR and change in NLR after the first cycle of chemotherapy (ΔNLR) were independent prognostic factors for overall survival (OS). We scored the risk considering NLR and ΔNLR and identified 4 risk groups with different prognosis (risk score 0 vs 1 vs 2 vs 3: OS 9.7 vs 7.9 vs 5.7 vs 2.6 months, HR 1 vs 1.329 vs 2.137 vs 7.915, respectively; P<0.001). In PET cohort, NLR and SUVmax were independently prognostic for OS. Prognostication model using both NLR and SUVmax could define 4 risk groups with different OS (risk score 0 vs 1 vs 2 vs 3: OS 11.8 vs 9.8 vs 7.2 vs 4.6 months, HR 1 vs 1.536 vs 2.958 vs 5.336, respectively; P<0.001). Conclusions: NLR and SUVmax as simple parameters of host immunity and metabolic activity of tumor cell, respectively, are independent prognostic factors for OS in MPC patients undergoing palliative chemotherapy. [ABSTRACT FROM AUTHOR]

Introduction: Body composition has emerged as a prognostic factor in cancer patients. We investigated whether sarcopenia at diagnosis and loss of skeletal muscle during palliative chemotherapy were associated with survival in patients with pancreatic cancer. Methods: We retrospectively reviewed the clinical outcomes of pancreatic cancer patients receiving palliative chemotherapy between 2003 and 2010. The cross-sectional area of skeletal muscle at L3 by computed tomography was analyzed with Rapidia 3D software. We defined sarcopenia as a skeletal muscle index (SMI)< 42.2 cm2/m2 (male) and < 33.9 cm2/m2 (female) using ROC curve. Results: Among 484 patients, 103 (21.3%) patients were sarcopenic at diagnosis. Decrease in SMI during chemotherapy was observed in 156 (60.9%) male and 65 (40.6%) female patients. Decrease in body mass index (BMI) was observed in 149 patients (37.3%), with no gender difference. By multivariate analysis, sarcopenia (P< 0.001), decreasedBMI and SMI during chemotherapy (P = 0.002, P = 0.004, respectively) were poor prognostic factors for overall survival (OS). While the OS of male patients was affected with sarcopenia (P< 0.001) and decreased SMI (P = 0.001), the OS of female patients was influenced with overweight at diagnosis (P = 0.006), decreased BMI (P = 0.032) and decreased SMI (P = 0.014). Particularly, while the change of BMI during chemotherapy did not have impact on OS within the patients with maintained SMI (P = 0.750), decrease in SMI was associated with poor OS within the patients with maintained BMI (HR 1.502; P = 0.002). Conclusions: Sarcopenia at diagnosis and depletion of skeletal muscle, independent of BMI change, during chemotherapy were poor prognostic factors in advanced pancreatic cancer. [ABSTRACT FROM AUTHOR]

Background: Lateral cervical lymph node (LCLN) metastasis, or pathologic N1b disease, is an important risk factor in papillary thyroid carcinoma (PTC). However, many patients have favorable prognosis even with pathologic N1b patients in clinical practice. The study aims to identify high- and intermediate-risk groups based on initial pathologic characteristics in these patients. Patients: This study included 518 classical PTC patients confirmed as pathologic N1b at initial surgery between 2001 and 2010. All patients underwent a single fixed activity (5.6 GBq) of radioactive I-131 remnant ablation. Results: Patients with a primary tumor larger than 4 cm, gross extrathyroidal extension, metastatic LN larger than 3 cm, or greater than 10 metastatic LCLN were classified as high-risk group. These comprehensive pathologic criteria were retrieved from cox proportional hazard models. Twenty two percent of patients (n = 113) were classified as high-risk and 78% (n = 405) as intermediate-risk group. Successful ablation was identified in only 32% of the patients in the high-risk group and 61% in the intermediate-risk group (p < 0.001). The difference between the two risk groups was independent to gender. There was a significant difference in disease-free survival between the high- and intermediate- risk N1b groups during 5.1 years of median follow-up (84% vs. 59%, p < 0.001). Distant metastasis was more prevalent in the high-risk group (20%) than in the intermediate-risk group (4%, p < 0.001). Conclusions: The prognosis of PTC patients with LCLN metastasis varies depending on initial pathologic characteristics. We proposed the comprehensive pathologic criteria for sub-classification of N1b into high- and intermediate-risk groups and this sub-classification may permit personalized management of N1b PTC patients. [ABSTRACT FROM AUTHOR]

Objective: Pulmonary function test (PFT) is a useful tool for an objective assessment of respiratory function. Impaired pulmonary function is critical for the survival and quality of life in patients with pulmonary metastases of solid cancers including thyroid cancer. This study aimed to evaluate clinical factors associated with severely impaired pulmonary function by serial assessment with PFT in patients with pulmonary metastasis of differentiated thyroid cancer (DTC) who received radioactive iodine treatment (RAIT). Patients: This retrospective study enrolled 31 patients who underwent serial PFTs before and after RAIT for pulmonary metastasis of DTC. We evaluated the risk factors for severe impairment of pulmonary function. Results: The median age of the patients was 44.1 years and 18 of them were female patients. Severe impairment of pulmonary function was observed in five patients (16%) after a median of three RAITs (cumulative I-131 activity = 20.4 GBq). These patients were older and more frequently had mild impairment of baseline pulmonary function, respiratory symptoms, or progressive disease compared with patients with stable pulmonary function. Neither cumulative dose nor number of RAIT was associated with decreased pulmonary function. Coexisting pulmonary diseases, presence of respiratory symptoms, and metastatic disease progression were significantly associated with severe decrease in forced vital capacity during follow-up (p =.047, p =.011, and p =.021, respectively). Conclusions: Pulmonary function was severely impaired during follow-up in some patients with pulmonary metastasis of DTC after a high-dose RAITs. Neither the number of RAIT nor the cumulative I-131 activity was associated with decreased pulmonary function. Serial PFT might be considered for some high-risk patients during follow-up. [ABSTRACT FROM AUTHOR]

Recent advance in sequencing technology has enabled comprehensive profiling of genetic alterations in cancer. We have established a targeted sequencing platform using next-generation sequencing (NGS) technology for clinical use, which can provide mutation and copy number variation data. NGS was performed with paired-end library enriched with exons of 183 cancer-related genes. Normal and tumor tissue pairs of 60 colorectal adenocarcinomas were used to test feasibility. Somatic mutation and copy number alteration were analyzed. A total of 526 somatic non-synonymous sequence variations were found in 113 genes. Among these, 278 single nucleotide variations were 232 different somatic point mutations. 216 SNV were 79 known single nucleotide polymorphisms in the dbSNP. 32 indels were 28 different indel mutations. Median number of mutated gene per tumor was 4 (range 0–23). Copy number gain (>X2 fold) was found in 65 genes in 40 patients, whereas copy number loss (